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Fig. 2 | Genome Biology

Fig. 2

From: 3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize

Fig. 2

Dynamic LoOCRs and histone modifications associated with differences in gene expression between ear and tassel. a MA plot showing differentially expressed genes between ear and tassel, with some known genes marked (highlighted dots with orange circles). Blue dots: 818 tassel-enriched genes; red dots: 434 ear-enriched genes. DEGs were defined with the following criteria: q value < 0.01, FC (fold change) > 1.5. bd Average signal intensities of ATAC-seq (b), H3K27me3 (c), and H3K4me3 (d) ± 3 kb around the transcription start sites (TSSs) of ear-enriched genes (upper panel) and tassel-enriched genes (lower panel). Ear-enriched genes showed more open chromatin states, stronger H3K4me3, and weaker H3K27me3 modifications in ear, and tassel-enriched genes showed the same results in tassel. The Wilcoxon test was used to test significance. e Number of differentially enriched local and distal OCRs, H3K4me3, and H3K27me3 modifications in ear and tassel. f, g Expression levels of genes with ear-enriched LoOCRs and H3K4me3 and ear-depleted H3K27me3 modifications in ear (f) and genes with tassel-enriched LoOCRs and H3K4me3 and tassel-depleted H3K27me3 modifications in tassel (g). The Wilcoxon test was used to test significance. ns—p > 0.05. h Venn diagram showing the overlap between tissue-enriched genes and genes associated with tissue-enriched LoOCRs. i, j Numbers of ear-enriched (i) and tassel-enriched (j) genes associated with different chromatin features that are differentially present between ear and tassel. km Examples of an ear-enriched gene, GT1 (branch suppression) (k), and tassel-enriched genes, SK1 (sex determination) (l) and ZmLOX3 (JA biosynthesis) (m), showing differences in their expression and chromatin states in ear and tassel. n FC (fold change) in the expression of tassel-enriched gene sets associated with single or combined chromatin state changes. The numbers of gene in different gene sets are shown at the bottom. K4, H3K4me3; K27, H3K27me3. *p < 0.05, **p < 0.01, ****p < 0.0001

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